<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<title>Rainbofilm Background</title>
<link href='http://fonts.googleapis.com/css?family=Molengo'
	rel='stylesheet' type='text/css'>
<link href='http://fonts.googleapis.com/css?family=Hammersmith+One'
	rel='stylesheet' type='text/css'>
<link href='http://fonts.googleapis.com/css?family=Alice'
	rel='stylesheet' type='text/css'>
<link href='http://fonts.googlea pis.com/css?family=Ovo'
	rel='stylesheet' type='text/css'>
<link href='http://fonts.googleapis.com/css?family=Federo'
	rel='stylesheet' type='text/css'>

<link href="modeling.css" rel="stylesheet" type="text/css">
<link href="global.css" rel="stylesheet" type="text/css">
<link href="template2.css" rel="stylesheet" type="text/css"><!-- include the Tools -->
<script src="http://cdn.jquerytools.org/1.2.6/full/jquery.tools.min.js"></script>
</head>

<body>
<div class="global">
<div class="header">
<div class="bgimg"></div>
<div class="bgpart1"></div>
<div class="bgpart2"></div>


<div class="banner">
<div class="logo"><img
	src="http://2011.igem.org/wiki/images/c/c9/Logo.png" width="200"
	height="200" /></div>
<div class="title"><img
	src="http://ung.igem.org/wiki/images/b/b3/Title.png" width="603"
	height="220" /></div>
<div class="igemlogo"><a target="_blank"
	href="http://2011.igem.org"><img
	src="http://2011.igem.org/wiki/images/e/e2/Igemlogo.png" width="180"
	height="150" /></a></div>
</div>
<!--banner-->
<div class="nav">
<ul id="topnav">
	<li><a id="P_Home" href="http://zjuchina.tk/index.html">Home</a></li>

	<li><a id="P_Project"
		href="http://zjuchina.tk/Project.html">Project</a> <!--Subnav Starts Here-->


	<!--Subnav Ends Here--></li>
	<li><a id="P_Team" href="http://zjuchina.tk/Team.html">Team</a>

	</li>
	<li><a id="P_Notebook"
		href="http://zjuchina.tk/Notebook.html">Notebook</a></li>
	<li><a id="P_HumanPractice"
		href="http://zjuchina.tk/Humanpractice.html">HumanPractice</a></li>
	<li id="search">
	<div id="searchbar">

	<div>
	<form action="http://www.google.com.hk/cse" id="cse-search-box"
		target="_blank">
	<div><input type="hidden" name="cx"
		value="005438704919531788579:zbfi5n-q5du" /> <input type="hidden"
		name="cof" value="FORID:10" /> <input type="hidden" name="ie"
		value="UTF-8" /> <input type="text" name="q" size="15" /> <input
		type="submit" name="sa" value="Search" /></div>
	</form>
	<script type="text/javascript"
		src="http://www.google.com/cse/brand?form=cse-search-box&lang=en"></script></div>
	</div>
	</li>
</ul>
</div>
<!--navbar--> <script type="text/javascript">
   document.getElementById('P_Team').onclick=function(){
	   document.getElementById('P_Te').style.display='block'

	    document.getElementById('P_Pr').style.display='none'
		document.getElementById('P_No').style.display='none'
		document.getElementById('P_Hu').style.display='none'
		<!-- document.getElementById('P_Pr').style.display='none' -->
	   };
	    document.getElementById('P_Project').onclick=function(){
	   document.getElementById('P_Pr').style.display='block'
	    document.getElementById('P_Te').style.display='none'
		document.getElementById('P_No').style.display='none'
		document.getElementById('P_Hu').style.display='none'
		<!-- document.getElementById('P_Pr').style.display='none' -->
	   };
	    document.getElementById('P_Notebook').onclick=function(){
	   document.getElementById('P_No').style.display='block'
	    document.getElementById('P_Pr').style.display='none'
		document.getElementById('P_Te').style.display='none'
		document.getElementById('P_Hu').style.display='none'
		<!-- document.getElementById('P_Pr').style.display='none' -->
	   };
	    document.getElementById('P_HumanPractice').onclick=function(){
	   document.getElementById('P_Hu').style.display='block'
	    document.getElementById('P_Pr').style.display='none'
		document.getElementById('P_No').style.display='none'
		document.getElementById('P_Te').style.display='none'
		<!-- document.getElementById('P_Pr').style.display='none' -->
	   };
	  
</script></div>
<!--header-->
<div id="contentwrapper">
<div class="main">
	<div class="bgcontainer">
	<div class="bgpart4">
    </div><!--bgpart4-->
	<div class="bgpart3"></div>
    </div>
<div class="leftulcontainer" id="orange">
<div id="leftul" class="leftul">
<div id="accordion">



<h4 id="try">Biofilm</h4>

<div class="pane"><a
	href="http://zjuchina.tk/Project.html">Background</a> <a
	href="http://zjuchina.tk/bio-Design.html">Design</a> <a
	href="http://zjuchina.tk/bio-modeling.html">Modeling</a> <a
	href="http://zjuchina.tk/bio-results.html">Results</a></div>

<h4 class="current">Rainbofilm</h4>

<div class="pane" style="display: block;"><a
	href="http://zjuchina.tk/rainbo-Background.html">Background</a>
<a href="http://zjuchina.tk/rainbo-Design.html">Design</a> <a
	href="http://zjuchina.tk/rainbo-modeling-v1.html">Modeling</a> <a
	href="http://zjuchina.tk/rainbo-Results.html">Results</a></div>

<h4>Sugarfilm</h4>

<div class="pane"><a
	href="http://zjuchina.tk/Sugar-background.html">Background</a> <a
	href="http://zjuchina.tk/Sugar-Design.html">Design</a> <a
	href="http://zjuchina.tk/Sugar-Modeling.html">Modeling</a> <a
	href="http://zjuchina.tk/Sugar-Future.html">Future</a></div>
<h4>Parts</h4>

<div class="pane"><a
	href="http://zjuchina.tk/BBa_I13602.html">PBBa_I13602</a> <a
	href="http://zjuchina.tk/BBa_K561000.html">BBa_K561000</a> <a
	href="http://zjuchina.tk/BBa_K561002.html">BBa_K561002</a> <a
	href="http://zjuchina.tk/BBa_K561003.html">BBa_K561003</a></div>
<h4>Achievements</h4>
<div class="pane"><a href="http://zjuchina.tk/data.html">Data
Page</a> <a href="http://zjuchina.tk/judging.html">Judging Form</a> <a
	href="http://zjuchina.tk/attribution.html">Attribution and
Contributions</a></div>

<h4>Tools</h4>

<div class="pane"><a href="http://zjuchina.tk/Tools.html">Tools</a>
</div>

<script> 
$(function() { 
 
$("#accordion").tabs("#accordion div.pane", {tabs: 'h4', effect: 'slide', initialIndex: null});
});
</script> <!-- Navigation scroll follow --> <script type="text/javascript">
        $(window).scroll(function () { 
            var scrollPos = $(window).scrollTop();
            if (scrollPos > 330) {
                $(".leftul").addClass("stickToTop");
            } else {
                $(".leftul").removeClass("stickToTop");
            }
     
        });
    </script></div>
<!--accordion--></div>
<!--leftul--></div>
<!--leftulcontainer-->

<div class="rightcontainer">
<div id="styleA" class="frame">
<div id="orange">
<h1>Background</h1>
<div id="framecontent">
<p>So far synthetic biologists have made tremendous effort in and
below the cell level, such as manipulating gene regulations, modifying
the metabolic pathways or producing specific proteins. However,
engineering work done in higher levels remains rare. This year,
ZJU-China has been focusing on the tissue level; we want to make cells
differentiated within a natural bacteria ‘tissue’, biofilm.</p>
<img src="http://2011.igem.org/wiki/images/4/45/Zjurainbo1.jpg"
	style="width: 500px; margin-left: 100px;" />
<blockquote>
<p id="ref" style="text-align: right;"><em>Rani, S. A. et al.
2007. J. Bacteriol. 189(11):4223-4233</em></p>
<p id="ref"><strong>FIG. 1</strong> Patterns of DNA synthesis in S.
    epidermidis colony biofilms. Panel A shows an unlabeled (no BrdU) colony biofilm probed with
    antibody. Panel B shows a colony biofilm labeled with BrdU under aerobic
    conditions. Panel C shows a colony biofilm labeled with BrdU under
    anaerobic conditions. Panel D shows a colony biofilm labeled with BrdU
    in an environment of pure oxygen. Green areas are due to BrdU
    incorporation into DNA and indicate active replication. Red areas are
    due to rhodamine B counterstaining that reveals the extent of the
    biomass independent of its activity. In each image, the membrane
    interface of the colony is on the bottom and the air interface is on the
    top.</p>
</blockquote>
<img src="http://2011.igem.org/wiki/images/a/ad/Zjurainbo2.jpg"
	style="width: 500px; margin-left: 100px; margin-top: 10px;" />
<blockquote>
<p id="ref" style="text-align: right;"><em>Rani, S. A. et al.
2007. J. Bacteriol. </em></p>
<p id="ref"><strong>FIG. 2</strong> Patterns of DNA synthesis in S.
epidermidis drip-flow (A) and capillary (B) biofilms and overlay of DNA
synthetic activity and protein synthetic activity in the same S. aureus
    colony biofilm (C and D)‏. In panels A and B, green areas are due to BrdU labeling and red
    areas are due to rhodamine B counterstain. In panel A, the substratum
    was on the bottom and the air interface was on the top. Flow was from
    top to bottom in panel B. In panel C, green areas are due to GFP
    expression and red areas are due to BrdU labeling. In panel C, the
    substratum was on the bottom, with the air interface on the top. Panel D
    shows the average fluorescence intensity along a linear transect across
    the section for the two signals. The position indicated on the x axis is
    arbitrary. The intensities indicated on the y axis of panel D are
    arbitrary as they result from automatic scaling by the digital image
    acquisition system.</p>
</blockquote>

<p>Biofilm is a complex self-organized bacteria community with
special spatial structure. One thing interesting about it is that from
the surface to the bottom, the bacteria maintain different physiological
states in a layered fashion. Both DNA synthesis and protein expression
is highly stratified within the biofilm. (Fig.1, Fig.2, Philip S.
Stewart, 2007) These varied layers can be characterized by gradients in
the concentrations of oxygen, nutrients, and metabolic waste products.
The external differences result in the differentiation of gene
transcription and protein expression patterns. Among all the factors,
oxygen is the most well studied one. (E. Werner, 2004).</p>
<table width="679" height="242" border="1" style="margin: auto;">
	<tr>
		<td style="padding: 5px;">
		<p><img src="zju-biofilmintro1a.png" width="150" height="200"
			alt="a" /></p>
		<p style="text-align: center;">Figure 1</p>
		</td>
		<td style="padding: 5px;">
		<p><img src="zju-biofilmintro1.1b.png" width="150" height="200"
			alt="b" /></p>
		<p style="text-align: center;">Figure 2</p>
		</td>
		<td style="padding: 5px;">
		<p><img src="zju-biofilmintro1.1c.png" width="150" height="200"
			alt="c" /></p>
		<p style="text-align: center;">Figure 3</p>
		</td>
	</tr>
</table>
<blockquote>
<p id="ref" style="text-align: right;"><em>Appl Environ
Microbiol. 2004 October; 70(10): 6188–6196</em></p>
<p><strong>FIG.3</strong> Oxygen concentration profiles for P.
aeruginosa colony biofilms. Triplicate data sets are shown for each
strain. Depth zero on the x axis corresponds to the air-colony
interface.</p>
</blockquote>
<p>We used different oxygen concentrations within the biofilm as
signals to induce the expression of different proteins and thus created
a new expression stratification system, as is indicated by the name
‘Rainbofilm’. It’s also the first attempt to utilize and modify bacteria
biofilm as an extracellular scaffold. Besides, biofilm’s adaptability
and resistance to environmental stress give our Rainbofilm a natural
edge as a new application in synthetic biology.</p>
<p>&nbsp;</p>
</div>


</div>
<!--orange--></div>
<!--frame--></div>
<!--rightcontainer-->

</div>
<!--main-->
<p style="clear: both"></p>
<div class="footer" id="footer"><a href="http://2011.igem.org/">
iGem 2011 Home Page</a> <a href="http://ung.igem.org/Special:Upload/">
Upload Files</a> <a
	href="http://2011.igem.org/wiki/index.php?title=Template:Zjucss_main&action=edit">Edit
CSS</a> <a href="http://ung.igem.org/Team_Wikis?year=2011"> Team Wikis</a> <a
	href="mailto:zjuigem@gmail.com?"><strong>Contact Us</strong></a></div>
</div>
<!--contentwrapper-->
</div>
</body>
</html>

